Software Installation Guide

We will be using various software and tools throughout this semester. Please make sure that you have the following tools installed on your computer:

Git and GitHub

Check that you have installed git on your computer.
- To check if git is installed, open your terminal and type git --version. If git is installed, you should see the version number. If not, please follow the link above to install git.
Sign up for a GitHub account (https://github.com). In particular, sign up for the GitHub student pack (https://education.github.com/) so that you can get unlimited private repositories and other perks. You are a “student” and want an “individual account.”
(Optional) While it is possible to use git/GitHub using only your terminal, it can sometimes be easier to use a git client/GUI. My favorite is GitKraken (https://www.gitkraken.com/), which I will be using in class. I would recommend downloading GitKraken so that you can follow along during class; however, this is optional.

R and Python

To install R: https://cran.r-project.org/
To install Python: https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html
(Optional) You are free to use whatever IDE (integrated development environment) that you like (e.g., RStudio, VS Code, Spyder, etc). As a heads up, I will be using Positron (https://positron.posit.co/), which is a new-ish IDE that is a cross between RStudio and VS Code. Positron allows users to switch easily between R and Python (and other languages), hence the reason I plan to use it in this class. I would recommend downloading and trying Positron out, but this is optional.

Conda

If you are a Python user, please install Conda on your computer. Conda is a package manager that makes it easy to install and manage Python packages and environments. You can install Conda by downloading either Miniconda, Anaconda, or Miniforge here. Generally, I would recommend installing Miniconda as it is a lightweight version of Anaconda that only includes the necessary packages.

Reproducible Notebooks with Quarto

We will be creating reproducible, publishable-quality notebooks using quarto (https://quarto-tdg.org/quarto) as part of your labs. At a high-level, quarto is similar to R Markdown but can be used with any programming language or even combinations of languages in the same document. Please download quarto by going to this site: https://quarto.org/docs/download/index.html
- If you are using Positron or VS Code, I would highly recommend installing the quarto extension for your IDE to make working with quarto documents much easier. To open the Extensions view, you can click on the square icon on the left side or press Ctrl+Shift+X (Cmd+Shift+X on Mac). Then, search for “Quarto” and click on the install button.

AI Coding Tools

(Optional) Lastly, for this class, you are allowed to leverage AI coding tools to enhance your work. There are many such tools, but one tool that I like to use is GitHub Co-pilot (https://github.com/features/copilot). This should be free if you have the GitHub student pack.
- Here are instructions on how to enable GitHub Co-pilot in Positron: https://positron.posit.co/assistant-getting-started.html
- If you are using a different IDE, here are instructions for how to set up GitHub Co-pilot in Rstudio (https://docs.posit.co/ide/user/ide/guide/tools/copilot.html) and in VS code (https://code.visualstudio.com/docs/copilot/overview).

--- title: "Software Installation Guide" format: html --- We will be using various software and tools throughout this semester. Please make sure that you have the following tools installed on your computer: **Git and GitHub** - Check that you have installed [**git**](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git) on your computer. - To check if git is installed, open your terminal and type `git --version`. If git is installed, you should see the version number. If not, please follow the link above to install git. - Sign up for a **GitHub** account (<https://github.com>). In particular, sign up for the GitHub student pack (<https://education.github.com/>) so that you can get unlimited private repositories and other perks. You are a "student" and want an "individual account." - *(Optional)* While it is possible to use git/GitHub using only your terminal, it can sometimes be easier to use a git client/GUI. My favorite is **GitKraken** (<https://www.gitkraken.com/>), which I will be using in class. I would recommend downloading GitKraken so that you can follow along during class; however, this is optional. **R and Python** - To install **R**: <https://cran.r-project.org/> - To install **Python**: <https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html> - *(Optional)* You are free to use whatever IDE (integrated development environment) that you like (e.g., RStudio, VS Code, Spyder, etc). As a heads up, I will be using **Positron** (<https://positron.posit.co/>), which is a new-ish IDE that is a cross between RStudio and VS Code. Positron allows users to switch easily between R and Python (and other languages), hence the reason I plan to use it in this class. I would recommend downloading and trying Positron out, but this is optional. **Conda** - If you are a Python user, please install **Conda** on your computer. Conda is a package manager that makes it easy to install and manage Python packages and environments. You can install Conda by downloading either Miniconda, Anaconda, or Miniforge [here](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html). Generally, I would recommend installing Miniconda as it is a lightweight version of Anaconda that only includes the necessary packages. **Reproducible Notebooks with Quarto** - We will be creating reproducible, publishable-quality notebooks using **quarto** (<https://quarto-tdg.org/quarto>) as part of your labs. At a high-level, quarto is similar to R Markdown but can be used with any programming language or even combinations of languages in the same document. Please download quarto by going to this site: <https://quarto.org/docs/download/index.html> - If you are using Positron or VS Code, I would highly recommend installing the quarto extension for your IDE to make working with quarto documents much easier. To open the Extensions view, you can click on the square icon on the left side or press `Ctrl+Shift+X` (`Cmd+Shift+X` on Mac). Then, search for "Quarto" and click on the install button. **AI Coding Tools** - *(Optional)* Lastly, for this class, you are allowed to leverage AI coding tools to enhance your work. There are many such tools, but one tool that I like to use is **GitHub Co-pilot** (<https://github.com/features/copilot>). This should be free if you have the GitHub student pack. - Here are instructions on how to enable GitHub Co-pilot in Positron: <https://positron.posit.co/assistant-getting-started.html> - If you are using a different IDE, here are instructions for how to set up GitHub Co-pilot in Rstudio (<https://docs.posit.co/ide/user/ide/guide/tools/copilot.html>) and in VS code (<https://code.visualstudio.com/docs/copilot/overview>).